This problem was introduced in version 3.12.0 by check-in [96ea990942].
A simple work-around is to drop the redundant "t1x" index. As far as
I can tell, this problem only comes up when there is an index on the
INTEGER PRIMARY KEY, as illustrated by t1x above.

drh added on 2016-05-06 03:56:34:

Another problem is that the SELECT statement below does a full table scan:

No indexes reference any columns of the table other than the primary key

DELETE with an OR in the WHERE clause

The OR clause uses the OP_Seek opcode to do a deferred seek of the main table.
That deferred seek is resolved at the first OP_Column. But if none of the
indexes ever reference a column (because they all only reference the integer
primary key) then the seek does not occur prior to the OP_Delete.

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